From chemistry-request@server.ccl.net Tue Jan 29 00:12:50 2002 Received: from uhura.curagen.com ([12.40.255.155]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0T5Coc18373 for ; Tue, 29 Jan 2002 00:12:50 -0500 Received: by uhura.curagen.com with Internet Mail Service (5.5.2653.19) id ; Tue, 29 Jan 2002 00:14:47 -0500 Message-ID: <715118539AC7D311A0DF009027DE6E190524AAB8@uhura.curagen.com> From: "Gusev, Vladimir" To: "'chemistry@ccl.net'" Subject: Fastest Intel/Amd Double Processor machine for MD Date: Tue, 29 Jan 2002 00:14:42 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hello, I am seeking information about assembling/buying a complete linux Intel or AMD-based system (double processor) that would be fastest at current standards (for Intel, I guess 2.2 GHz, 0.13 micron processor is mandatory). Please let me know about available options - complete systems, parts, overclocking experiences etc, as well as benchmarks. This is to run an MD codes such as for example Gromacs to model protein confirmations.The replies will be summarized. Thank you. Vladimir LEGAL NOTICE - Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this e-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. From chemistry-request@server.ccl.net Tue Jan 29 01:17:30 2002 Received: from web21309.mail.yahoo.com ([216.136.173.254]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0T6HUc20034 for ; Tue, 29 Jan 2002 01:17:30 -0500 Message-ID: <20020129061725.5923.qmail@web21309.mail.yahoo.com> Received: from [208.241.25.130] by web21309.mail.yahoo.com via HTTP; Mon, 28 Jan 2002 22:17:25 PST Date: Mon, 28 Jan 2002 22:17:25 -0800 (PST) From: Richard SMITH Subject: Intro materials To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Friends: I have been asked to give a presentation in our chemistry department on the topic of Computer Aided Drug Discovery. I would appreciate to receive your inputs in choosing some important papers (as this is for a genral chemistry audiance) like the most important contributions in the area of CADD, QSAR, Screening, and hit/lead/drug developmental stages. I would also appreciate in receiving sharable powerpoint (ppt), postcript, pdf or any image files on these topics (containing introductory materials, eye-capturing pictures and so-on). Thanks very much. With Regards Smith __________________________________________________ Do You Yahoo!? Great stuff seeking new owners in Yahoo! Auctions! http://auctions.yahoo.com From chemistry-request@server.ccl.net Tue Jan 29 01:36:33 2002 Received: from mdl.ipc.pku.edu.cn (IDENT:postfix@[162.105.177.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0T6aVc20589 for ; Tue, 29 Jan 2002 01:36:32 -0500 Received: by mdl.ipc.pku.edu.cn (Postfix, from userid 2556) id ECF8A2B670; Tue, 29 Jan 2002 14:39:49 +0800 (CST) Received: from localhost (localhost [127.0.0.1]) by mdl.ipc.pku.edu.cn (Postfix) with ESMTP id E7F1D2B66F for ; Tue, 29 Jan 2002 14:39:49 +0800 (CST) Date: Tue, 29 Jan 2002 14:39:49 +0800 (CST) From: Gao Ying To: CHEMISTRY@ccl.net Subject: how to convert .rdf to .sdf file? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer, Could you kindly tell me how to convert .rdf to .sdf file. Is there any program to do such work? Thanks in advance! Gao Ying From chemistry-request@server.ccl.net Tue Jan 29 03:02:17 2002 Received: from ingfi1.ing.unifi.it ([150.217.10.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0T82Ec24934 for ; Tue, 29 Jan 2002 03:02:15 -0500 Received: from dsi.unifi.it (glycine.dsi.unifi.it [150.217.15.192]) by ingfi1.ing.unifi.it (8.11.6/8.11.6) with ESMTP id g0T80Ch29911; Tue, 29 Jan 2002 09:00:14 +0100 Message-ID: <3C565850.3040103@dsi.unifi.it> Date: Tue, 29 Jan 2002 09:07:44 +0100 From: Addis User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.5) Gecko/20011023 X-Accept-Language: en MIME-Version: 1.0 To: "Dr. S. Shapiro" CC: chemistry@ccl.net Subject: Re: CCL references question References: <200201251354.OAA19130@zisp0103.unizh.ch> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dr. S. Shapiro wrote: > Dear Madam: > > Can you please sent me the complete citations (authors, title, journal, > volume, pages, year) for these three articles? > > Thanks, > > S. Shapiro > toukie@zui.unizh.ch > > P.-S.: Please indicate the presence of vowels with umlauts using parentheses, > e.g. U(e)ber, mo(e)chte, Ma(e)dchen. > A. Einstein, "U(e)ber die von der molekular-kinetischen Theorie der Wa(e)rme geforderte Bewegung von in ruhenden Flu(e)ssigkeiten suspendierten Teilchen", Annalen der Physik vol. 17, p. 549 (1905) A. Einstein, "Zur Theorie der Brownschen Bewegung", Annalen der Physik vol. 19, p. 371 (1906) M. v. Smoluchowski, "Kinetische Theorie der Brownschen Bewegung", Annalen der Physik vol. 21, p. 756 (1906) Bernardetta Addis From chemistry-request@server.ccl.net Tue Jan 29 07:25:47 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TCPlc30852 for ; Tue, 29 Jan 2002 07:25:47 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 16VXHi-0003xH-00; Tue, 29 Jan 2002 12:22:46 +0000 Date: Tue, 29 Jan 2002 12:22:46 +0000 (GMT) From: Szilveszter Juhos To: "J. Zheng" cc: chemistry@ccl.net Subject: Re: CCL:help: pdb --> charmm In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 28 Jan 2002, J. Zheng wrote: > 1) open read card unit 10 name 7LYZ.pdb > when I type above command, charmm said there is no title. Try run from script file, it will be more convenient. Prepare your file like: * This is a title, write here * something useful and end with a line * with only asterix in it * ! it is a comment ..do your stuff here... And run: $ charmm.exe < infile.scr But you will have problems with amino acids with undefined protonation state if you are reading straight from PDB. If you do not have access to Accelrys software/docs, try: http://www.scripps.edu/brooks/ Hope it helps (I think starting with a smaller molecule would be easier). Szilva From chemistry-request@server.ccl.net Tue Jan 29 11:02:10 2002 Received: from ccusv8.unical.it ([160.97.7.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TG23c02962 for ; Tue, 29 Jan 2002 11:02:04 -0500 Received: from chpcrs6 (chpcrs6.chimica.unical.it [160.97.42.132]) by ccusv8.unical.it (8.11.2/8.11.2) with SMTP id g0TFdsc04841 for ; Tue, 29 Jan 2002 16:39:55 +0100 Message-ID: <004101c1a8df$1441e240$842a61a0@chpcrs6> From: "Nino Russo" To: Subject: nato-asi event Date: Tue, 29 Jan 2002 17:07:40 +0100 NATO Advanced Study Institute (ASI) on Metal-Ligand interactions in molecular-, nano-, micro-, and macro-systems in complex environments Cetraro (CS), Italy September 1-12, 2002 Director: Prof. Nino Russo Dipartimento di Chimica Università della Calabria I-87030 Arcavacata di Rende Italy Co-Director: Prof. Malgorzata Witko Institute of Catalysis Polish Academy of Sciences 30239 Cracow Poland Organizing Committee -Nino Russo Dipartimento di Chimica, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy nrusso@unical.it -Malgorzata Witko Institute of Catalysis, Polish Academy of Sciences, ul Niezapominajek, 30239 Cracow, Poland nwitko@cyf-kr.edu.pl -Dennis R. Salahub Steace Institute for Molecular Sciences, NRC, 100 Sussex Drive, Ottawa K1A OR6 Canada dennis.salahub@nrc.ca -Hans Joachim Freund Fritz-Haber Institute, Max Plank Gesellschaft, Chemische Physik, Faradayweg 4-6, D-14195 Berlin, Germany freund@FHI-berlin.mpg.de -Julius Jellinek Chemistry Division, Argonne National Laboratory, Argonne, IL 60439, USA jellinek@anlchm.chm.anl.gov Lecturers A. Belcher University of Texas, Austin, USA H. J. Freund* Fritz-Haber Institute, Berlin, Germany U. Heiz University of Lousanne, Switzerland C. Henry* CNRS, Luminy, France J. Jellinek,* Argonne National Laboratories, Argonne, USA G. Ozin University of Toronto, Canada M. Pettitt University of Texas, Huston, USA M. Ratner Northwestern University, USA E. Rizzarelli* Università di Catania, Catania, Italy N. Russo* Università della Calabria, Arcavacata di Rende, Italy D. R. Salahub* Steace Institute for Molecular Science-NRC, Ottawa, Canada R. Schlogl* Fritz-Haber Institute, Berlin, Germany D. York University of Minnesota, USA M. Witko* Institute of Catalysis, Polish Acad. of Sci., Cracow, Poland J. Webb* Mudoch University, Australia In addition a series of Special Research Seminars will be taken by: M. Ghedini Università della Calabria, Arcavacata di Rende, Italy E. Drioli Università della Calabria, Arcavacata di Rende, Italy J. Ugalde Universidad del Pais Vasco, Spain I. Bertini Università di Firenze, Italy C. Mijoule Université de Toulose, France A. Grand CEA, Grenoble, France P. Gerling Bruxelles, Belgium G. Frenking Philipps Universitat, Marburg, Germany K. Hermann FHI, Berlin, Germany Topics Transition Metal Chemistry Material Sciences Catalysis Surface Science Bio-inorganic Chemistry Molecular Dynamics Density Functional, ab-initio and semiempirical methods Location and Venue The ASI will take place at the Grand Hotel San Michele ( http://www.sanmichele.it ) in Cetraro, Calabria, a beautiful four star hotel on the sea with all conveniences, a private beach, golf and tennis, and a well-earned reputation for their meals. The closest airport is at Lametia Terme about an hour's flight south of Rome. A bus service will be arranged from Lametia Terme Airport to the ASI side, with stops at Paola railway station (6 hours from Rome and 4 > from Naples with an Intercity) for those who arrive by train. Further information on the train schedule can be obtained at www.trenititalia.it . Cars may be rented at Lametia Terme airport. Besides the breathtaking beaches, mountains and sea-scapes, a short trip may be made to Reggio Calabria (an hour and half by car from Cetraro) and the famous archaeological museum (the Riace bronzes are nothing short of magnificent) and a short boat ride (two hours by boat) from there to Aeolian Islands with their active volcanoes and more superb beaches. General Informations A NATO-ASI is an International "summer school" of eleven working days. Lectures and special research seminars are aimed at the post-doctoral level. The ASI participants may be senior graduate students, post-doctoral fellows, University Faculty members, governments or industrial researchers. Attendance will be limited to about 90 students chosen on the basis of their interest and contributions to the subject area, the potential benefit to them and to the ASI from their attendance, and so as to the achieve a balance of nationalities. Tuition. There will be no tuition fees for participants from academic institutions. Participants from industry will be asked to pay a tuition fee of $ US 300 or, better, to have their companies make a more substantial contribution to the school (with appropriate recognition in the program and publication). Room and board. Lodging will be at the Grand Hotel San Michele. With only a few exceptions, rooms will be assigned double occupancy. The cost of room and full board for the 12 nights is 568 Euro (about $ US 550). It is hoped that participants institutions will cover most or all of the living expenses. However, the grand from NATO and other support should allow significant subsidies to those who would otherwise be unable to attend. Travel support. There is a possibility of limited support. Application Those wishing to attend should send a letter by mail, fax or electronic mail. This should specify: - date and place of birth - sex - nationality - academic qualifications - present position and place of work - a brief statement of ongoing research and publications relevant to the theme of the ASI - PhD student and postdocs should also have send a brief letter from their research director supporting their attendance - Those requesting financial aid should state how much and provide a brief justification. The closing date for application is june 30, 2002. After that date, applications will be reviewed on space-available basis. Application should be send to Prof. Nino Russo NATO-ASI Director Dipartimento di Chimica Università della Calabria I-87036 Arcavacata di Rende (CS) Italy Tel- +39-0984-492106; fax: +39-0984-492044: e.mail: russo@unical.it From chemistry-request@server.ccl.net Tue Jan 29 14:03:56 2002 Received: from jilau1.Colorado.EDU ([128.138.140.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TJ3uc07320 for ; Tue, 29 Jan 2002 14:03:56 -0500 Received: from colorado.edu (ixion.Colorado.EDU [128.138.107.182]) by jilau1.Colorado.EDU (8.11.6/8.11.6/UnixOps+Hesiod) with ESMTP id g0TJ3md220830 for ; Tue, 29 Jan 2002 12:03:48 -0700 (MST) Sender: thompsma@jilau1.Colorado.EDU Message-ID: <3C56F214.4DA27D8A@colorado.edu> Date: Tue, 29 Jan 2002 12:03:48 -0700 From: Matt Thompson Organization: JILA X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.9-13smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:Gaussian Scan Output Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit This is a very minor problem, but one that would make my life easier. I am doing potential energy surface scans in g98(A.7) and am wondering how I can get the output summary at the end of the scan to display more/different columns. That is, I am doing CCSD(T) and QCISD(T) scans for comparisons, but while the QCISD(T) scan will summarize the final QCISD(T) results in a column, the CCSD(T) only goes to MP4SDTQ and doesn't display the CCSD* results. Is this just a limitation of the program itself, or is there an option I can select? Thank you, Matt Thompson thompsma@colorado.edu -- "And isn't sanity really just a one-trick pony, anyway? I mean, all you get is one trick, rational thinking, but when you're good and crazy, ooh ooh ooh, the sky's the limit!" -- The Tick TheMatt -- http://ucsub.colorado.edu/~thompsma/Home.html From chemistry-request@server.ccl.net Tue Jan 29 15:28:16 2002 Received: from smtpsrv1.isis.unc.edu ([152.2.1.138]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TKSGc08896 for ; Tue, 29 Jan 2002 15:28:16 -0500 Received: from chastity.isis.unc.edu (chastity.isis.unc.edu [152.2.1.128]) by smtpsrv1.isis.unc.edu (8.9.3/8.9.1) with ESMTP id PAA08601 for ; Tue, 29 Jan 2002 15:28:07 -0500 (EST) Received: (from feng@localhost) by chastity.isis.unc.edu (8.9.3/8.9.3) id PAA174918; Tue, 29 Jan 2002 15:28:07 -0500 (EST) Date: Tue, 29 Jan 2002 15:28:06 -0500 From: Jun Feng X-Sender: feng@chastity.isis.unc.edu To: chemistry@ccl.net Subject: Question about Delphi Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I happen to run some calculations using Delphi, but I found some problems here. I set the charge of one atom in the molecule to +1.0, and all charges on other atoms to 0.0. To get the solvation energy, two calculations were performed, one using D_interior=1.0,D_solvent=1.0, another one using D_interior=1.0,D_solvent=80.0. Fill percentage is set to 23%. Surprisingly I found that solvation energy calculated by difference of total grid energys no longer equal to that calculated by reaction field energy. Anyone have any idea of this? Jun From chemistry-request@server.ccl.net Tue Jan 29 12:16:21 2002 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0THGKc04860 for ; Tue, 29 Jan 2002 12:16:21 -0500 Received: from unibas.ch (filou.chemie.unibas.ch [131.152.112.19]) by igor.urz.unibas.ch (PMDF V6.1 #38375) with ESMTP id <0GQP001M0MN3KI@igor.urz.unibas.ch> for chemistry@ccl.net; Tue, 29 Jan 2002 18:16:15 +0100 (MET) Date: Tue, 29 Jan 2002 18:15:54 +0100 From: Stanislav Ivan Subject: StepSize To: chemistry@ccl.net Message-id: <3C56D8C9.B54A4F3D@unibas.ch> MIME-version: 1.0 X-Mailer: Mozilla 4.75 [en] (WinNT; U) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-Accept-Language: en Dear CCL'rs, I tried to reduce the step size during optimisation in gaussian98 - opt=(StepSize=10) but but it doesn't work.I allways get the error message about this keyword.But in the g98 manual I found exactly this keyword. All comments are appreciated. Stan -- Stanislav Ivan Institut für Organische Chemie St. Johanns Ring 19 4056 Basel Switzerland Tel.: (+41) (61) 267 11 44 E-mail: stanislav.ivan@unibas.ch From chemistry-request@server.ccl.net Tue Jan 29 14:40:33 2002 Received: from access.etsu.edu ([151.141.99.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TJeXc08195 for ; Tue, 29 Jan 2002 14:40:33 -0500 Received: from dmc ([151.141.29.51]) by ACCESS.ETSU.EDU (PMDF V6.1 #39282) with SMTP id <01KDNATP66QG9BWAWQ@ACCESS.ETSU.EDU> for chemistry@ccl.net; Tue, 29 Jan 2002 14:40:24 -0500 (EST) Date: Tue, 29 Jan 2002 13:41:20 -0500 From: David Close Subject: g98 LINUX installation? X-Sender: closed@access.etsu.edu To: chemistry@ccl.net Message-id: <3.0.6.32.20020129134120.009b0e90@access.etsu.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT CCL: Last week a subscriber asked for help installing G98 on a system using Linux 7.x. I would like to see the replies to this question, but have been unable to obtain them. There were some suggestions posted to CCL on compiling the FORTRAN code. I have the compiled LINUX version of G98, and need help with installation. I have the program running on RedHat 6.2, but am having problems getting this to work on RedHat 7.1 Thanks, Dave Close. From chemistry-request@server.ccl.net Tue Jan 29 20:41:08 2002 Received: from mx03.gis.net ([208.218.130.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0U1f8c19579 for ; Tue, 29 Jan 2002 20:41:08 -0500 Received: from [216.243.61.220] ([216.243.61.220]) by mx03.gis.net; Tue, 29 Jan 2002 20:40:52 -0500 (EST) Mime-Version: 1.0 X-Sender: (Unverified) Message-Id: In-Reply-To: References: Date: Tue, 29 Jan 2002 20:38:42 -0500 To: Gao Ying From: Jonathan Brecher Subject: Re: CCL:how to convert .rdf to .sdf file? Cc: CHEMISTRY@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Could you kindly tell me how to convert .rdf to .sdf file. >Is there any program to do such work? You can no more convert an .rdf file to an .sdf file than you can convert a cube to a square. RD files contain data types that SD files cannot. For more information, don't post to a mailing list -- go directly to the source (gee, have I said that before?) -- which in this case is http://www.mdli.com/downloads/ctfile/ctfile_subs.html If you've *got* to do that conversion and you don't care how much data you lose, there are many programs that will do the conversion as best as the file formats will permit. MDL's own ISIS/Base and our CS ChemFinder come to mind. There are likely others, but it hardly matters given the circumstances. Jonathan Brecher CambridgeSoft Corporation jsb@cambridgesoft.com -- From chemistry-request@server.ccl.net Tue Jan 29 17:07:14 2002 Received: from gate-sl1.mdli.com ([208.200.221.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TM7Ec10973 for ; Tue, 29 Jan 2002 17:07:14 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id OAA19986 for ; Tue, 29 Jan 2002 14:07:09 -0800 (PST) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1.mdli.com via smap (V2.1) id xma019984; Tue, 29 Jan 02 14:07:07 -0800 Received: from blackbird.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id OAA51744; Tue, 29 Jan 2002 14:07:07 -0800 (PST) Received: from mdli.com (localhost [127.0.0.1]) by blackbird.mdli.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id OAA18596 for ; Tue, 29 Jan 2002 14:07:07 -0800 (PST) Sender: jdurant@mdli.com Message-ID: <3C571D0A.EAA15128@mdli.com> Date: Tue, 29 Jan 2002 14:07:06 -0800 From: Joseph Durant X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:how to convert .rdf to .sdf file? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! In general the two file types are not interconvertable. .rdf files normally contain reactions and associated data, and .sdf files contain only molecules with associated data. You can only interconvert those .rdf files which contain only molecules, with straightforward associated data. You can get more information from the spec documents for the MDL file formats: http://www.mdli.com/downloads/ctfile/ctfile_subs.html Hope this helps. Joe Gao Ying wrote: > > Dear CCLer, > > Could you kindly tell me how to convert .rdf to .sdf file. > Is there any program to do such work? > > Thanks in advance! > > Gao Ying > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Joe Durant jdurant@mdli.com MDL Information Systems 14600 Catalina Street, San Leandro, CA 94577 voice: (510) 357-2222 x 1331 or (510) 895-1313 FAX: (510) 614-3616 -------------- If Bill Gates had a nickel for every time Windows crashed... ... oh wait, he does. From chemistry-request@server.ccl.net Tue Jan 29 16:54:51 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TLspc10775 for ; Tue, 29 Jan 2002 16:54:51 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g0TLslc12561 for ; Tue, 29 Jan 2002 15:54:47 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g0TLskg10912 for ; Tue, 29 Jan 2002 15:54:46 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Tue, 29 Jan 2002 15:54:46 -0600 (CST) From: Jim Phillips To: chemistry@ccl.net Subject: NAMD 2.4b1 (Parallel MD) Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, NAMD is a molecular dynamics program, file compatible with X-PLOR, CHARMM, and AMBER, scalable to hundreds of processors, and available as source code or binaries for a variety of platforms, free of charge. Try it out! -Jim +--------------------------------------------------------------------+ | | | NAMD 2.4b1 Release Announcement | | | +--------------------------------------------------------------------+ January 25, 2002 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.4b1 has several advantages over NAMD 2.3: - Greatly improved parallel scaling with particle mesh Ewald. - GROMACS ASCII topology and coordinate input file compatibility. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html The Theoretical Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Tue Jan 29 15:37:55 2002 Received: from smtp.noos.fr ([212.198.2.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0TKbsc09178 for ; Tue, 29 Jan 2002 15:37:55 -0500 Received: (qmail 4314892 invoked by uid 0); 29 Jan 2002 16:44:27 -0000 Received: from unknown (HELO nan-portail-06.admin.noos.net) ([192.168.17.194]) (envelope-sender ) by 192.168.17.133 (qmail-ldap-1.03) with SMTP for ; 29 Jan 2002 16:44:27 -0000 Received: (from wwwuser@localhost) by nan-portail-06.admin.noos.net (8.10.2+Sun/8.10.2) id g0TGiQC20551; Tue, 29 Jan 2002 17:44:26 +0100 (MET) Date: Tue, 29 Jan 2002 17:44:26 +0100 (MET) Message-Id: <200201291644.g0TGiQC20551@nan-portail-06.admin.noos.net> To: chemistry@ccl.net Subject: G98 : massage keyword and fractional nuclear charges From: "remoi remoi" MIME-Version: 1.0 X-Mailer: NOOSwebmail v2 Reply-to: sardinhas@noos.fr Content-Type: text/plain; charset="iso-8859-1" Dear CCL, Is it possible to assign a non-integer charge to a nucleus with the massage keyword? (a mere "3 Nuc 7.25" will give nucleus #3 Z=7 and not Z=7.25...) Maybe other programs allow these "experiments" ? Thanks a lot